Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,531,610	3	.	A	72.7%	45.5 / 13.2	22	coding (240/360 nt)	SAUSA300_RS13005	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/6);  new base A (0/16);  total (0/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.36e-01

AATCCGCATCATGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑TCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCATAGACATAAATATTAGC  >  NC_007793/2531516‑2531678                                                                                                  |                                                                     aaTCCGCATCATGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑tcatc                                                                 <  1:1539157/100‑1 (MQ=255)    ccGCATCATGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑Tcatcatc                                                              <  1:1333967/100‑2 (MQ=255)    ccGCATCATGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑Tcatcatc                                                              <  1:1362/100‑2 (MQ=255)     cGCATCATGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑Tcatcatcc                                                             <  1:649262/100‑3 (MQ=255)        atcatGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑Tcatcatcatcc                                                          <  1:624301/100‑6 (MQ=255)          catGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑TCATCATCATTCac                                                        <  1:1245215/100‑2 (MQ=255)             gttgttGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑Tcatcatcattactcaa                                                     <  1:1971734/100‑11 (MQ=255)                  tgATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGTATAATAATGCACTTCATCATCATTACTCAAAGGta                                                   <  1:2399888/100‑2 (MQ=255)                     taataTCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTtat                                                <  1:4981454/100‑1 (MQ=255)                      cttccgatctcTAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTtata                                               <  1:230166/93‑1 (MQ=255)                      cttccgatctcGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTtata                                               <  1:4467641/93‑1 (MQ=255)                      aataTCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTtata                                               <  1:3902856/100‑1 (MQ=255)                      aataTCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTtata                                               <  1:474631/100‑1 (MQ=255)                      aataTCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTtata                                               <  1:4256835/100‑1 (MQ=255)                      aataTCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTtata                                               <  1:3151882/100‑1 (MQ=255)                                                   tatGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCAt                  <  1:3706397/100‑1 (MQ=255)                                                   tatGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCAt                  <  1:2801769/100‑1 (MQ=255)                                                   tatGATACACGTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCAt                  <  1:5343383/100‑1 (MQ=255)                                                             gTTTATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCATAGACATAAat        <  1:2155740/100‑1 (MQ=255)                                                                tATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCATAGACATAAATAtt     <  1:3943023/100‑1 (MQ=255)                                                                tATCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCATAGACATAAATAtt     <  1:2588409/100‑1 (MQ=255)                                                                  tCACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCATAGACATAAATATTAg   <  1:3004273/100‑1 (MQ=255)                                                                   cACTAAAATCATATGCATAATAATGCACTTCATCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCATAGACATAAATATTAGc  <  1:4948526/100‑1 (MQ=255)                                                                                                  |                                                                     AATCCGCATCATGTTGTTGATAATATCGTCTCGAATCAAAATCTTGCTTATATGATACACGTTTATCACTAAAATCATATGCATAATAATGCACT‑‑‑TCATCATTACTCAAAGGTTTATAAGCTAAAATGATAATTTTATCCTTATCATAGACATAAATATTAGC  >  NC_007793/2531516‑2531678

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑